File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23120ms, 88.82% of 26031ms total Dropped 813 nodes (cum <= 130.16ms) flat flat% sum% cum cum% 0 0% 0% 25924ms 99.59% __libc_start_call_main 0 0% 0% 25924ms 99.59% __libc_start_main_impl 0 0% 0% 25924ms 99.59% _start 0 0% 0% 25906ms 99.52% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 25906ms 99.52% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 25906ms 99.52% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 25906ms 99.52% main 0 0% 0% 25871ms 99.39% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 25871ms 99.39% CxxTest::TestRunner::runTest (inline) 0 0% 0% 25871ms 99.39% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 3ms 0.012% 0.012% 25863ms 99.35% AbstractCellBasedSimulation::Solve 1ms 0.0038% 0.015% 14493ms 55.68% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.015% 10152ms 39.00% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0038% 0.019% 8900ms 34.19% NodeBasedCellPopulation::Update 1ms 0.0038% 0.023% 8377ms 32.18% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.012% 0.035% 8180ms 31.42% AbstractNumericalMethod::ComputeForcesIncludingDamping 1006ms 3.86% 3.90% 7432ms 28.55% RepulsionForce::AddForceContribution (partial-inline) 4ms 0.015% 3.91% 6775ms 26.03% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 3.91% 5776ms 22.19% OffLatticeSimulation::ApplyBoundaries 2372ms 9.11% 13.03% 5427ms 20.85% std::_Rb_tree::_M_lower_bound (inline) 29ms 0.11% 13.14% 5191ms 19.94% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.023% 13.16% 4952ms 19.02% std::__sort (inline) 0 0% 13.16% 4952ms 19.02% std::sort (inline) 297ms 1.14% 14.30% 4284ms 16.46% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 165ms 0.63% 14.94% 4089ms 15.71% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 3ms 0.012% 14.95% 4051ms 15.56% AbstractCellPopulation::Iterator::operator++ (inline) 207ms 0.8% 15.74% 4038ms 15.51% AbstractCellPopulation::Iterator::IsRealCell (inline) 293ms 1.13% 16.87% 3522ms 13.53% std::_Rb_tree::find (inline) 0 0% 16.87% 3522ms 13.53% std::map::find (inline) 38ms 0.15% 17.01% 3406ms 13.08% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 241ms 0.93% 17.94% 3001ms 11.53% std::__introsort_loop 87ms 0.33% 18.27% 2941ms 11.30% AbstractMesh::GetNode 70ms 0.27% 18.54% 2937ms 11.28% PlaneBoundaryCondition::ImposeBoundaryCondition 66ms 0.25% 18.80% 2921ms 11.22% NodesOnlyMesh::GetNodeOrHaloNode 259ms 0.99% 19.79% 2870ms 11.03% std::map::operator[] (partial-inline) 243ms 0.93% 20.73% 2858ms 10.98% NodesOnlyMesh::SolveNodeMapping 55ms 0.21% 20.94% 2839ms 10.91% PlaneBoundaryCondition::VerifyBoundaryCondition 2727ms 10.48% 31.41% 2727ms 10.48% std::_Rb_tree::_S_right (inline) 8ms 0.031% 31.44% 2664ms 10.23% std::__unguarded_partition_pivot (inline) 131ms 0.5% 31.95% 2467ms 9.48% AbstractCellPopulation::GetLocationIndexUsingCell 813ms 3.12% 35.07% 2410ms 9.26% std::__unguarded_partition (inline) 0 0% 35.07% 2238ms 8.60% std::_Rb_tree::lower_bound (inline) 0 0% 35.07% 2238ms 8.60% std::map::lower_bound (inline) 146ms 0.56% 35.63% 2174ms 8.35% DistributedBoxCollection::AddPairsFromBox 2ms 0.0077% 35.64% 1942ms 7.46% std::__final_insertion_sort (inline) 20ms 0.077% 35.72% 1795ms 6.90% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 24ms 0.092% 35.81% 1762ms 6.77% AbstractCellPopulation::GetCellUsingLocationIndex 138ms 0.53% 36.34% 1730ms 6.65% std::__unguarded_insertion_sort (inline) 817ms 3.14% 39.48% 1558ms 5.99% std::__unguarded_linear_insert (inline) 28ms 0.11% 39.58% 1239ms 4.76% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 43ms 0.17% 39.75% 1225ms 4.71% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 39.75% 1206ms 4.63% NodeBasedCellPopulation::UpdateCellProcessLocation 1166ms 4.48% 44.23% 1166ms 4.48% __gnu_cxx::__normal_iterator::operator-- (inline) 6ms 0.023% 44.25% 1071ms 4.11% DistributedBoxCollection::CalculateBoundaryNodePairs 34ms 0.13% 44.38% 1058ms 4.06% boost::detail::shared_count::~shared_count (inline) 0 0% 44.38% 1058ms 4.06% boost::shared_ptr::~shared_ptr (inline) 8ms 0.031% 44.41% 1030ms 3.96% boost::numeric::ublas::vector_assign (inline) 989ms 3.80% 48.21% 1009ms 3.88% boost::detail::sp_counted_base::release 307ms 1.18% 49.39% 918ms 3.53% __dynamic_cast 513ms 1.97% 51.36% 898ms 3.45% NodeAttributes::AddNeighbour 221ms 0.85% 52.21% 879ms 3.38% boost::numeric::ublas::indexing_vector_assign 331ms 1.27% 53.48% 815ms 3.13% DistributedBoxCollection::CalculateContainingBox (partial-inline) 24ms 0.092% 53.57% 801ms 3.08% std::_Rb_tree_const_iterator::operator++ (inline) 103ms 0.4% 53.97% 757ms 2.91% AbstractMesh::GetVectorFromAtoB 0 0% 53.97% 739ms 2.84% AbstractCellPopulation::WriteResultsToFiles 718ms 2.76% 56.73% 718ms 2.76% std::_Rb_tree_increment 19ms 0.073% 56.80% 701ms 2.69% CellPropertyCollection::GetPropertiesType (inline) 701ms 2.69% 59.49% 701ms 2.69% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 1ms 0.0038% 59.50% 694ms 2.67% AbstractCentreBasedCellPopulation::GetDampingConstant 72ms 0.28% 59.77% 687ms 2.64% std::__new_allocator::allocate (inline) 3ms 0.012% 59.79% 672ms 2.58% boost::numeric::ublas::c_vector::operator= (inline) 40ms 0.15% 59.94% 658ms 2.53% std::__copy_move::__copy_m (inline) 0 0% 59.94% 658ms 2.53% std::__copy_move_a (inline) 0 0% 59.94% 658ms 2.53% std::__copy_move_a1 (inline) 0 0% 59.94% 658ms 2.53% std::__copy_move_a2 (inline) 0 0% 59.94% 658ms 2.53% std::allocator_traits::allocate (inline) 0 0% 59.94% 658ms 2.53% std::copy (inline) 0 0% 59.94% 647ms 2.49% AbstractCellBasedSimulation::DoCellBirth 0 0% 59.94% 646ms 2.48% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 39ms 0.15% 60.09% 637ms 2.45% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 60.09% 620ms 2.38% boost::numeric::ublas::norm_2 (inline) 496ms 1.91% 62.00% 620ms 2.38% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 62.00% 620ms 2.38% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 62.00% 612ms 2.35% std::_Rb_tree::_M_create_node (inline) 27ms 0.1% 62.10% 607ms 2.33% operator new 0 0% 62.10% 603ms 2.32% AbstractCellBasedSimulation::DoCellRemoval (inline) 593ms 2.28% 64.38% 593ms 2.28% __gnu_cxx::__normal_iterator::operator++ (inline) 588ms 2.26% 66.64% 588ms 2.26% __memcpy_evex_unaligned_erms 0 0% 66.64% 587ms 2.26% std::_Rb_tree::_M_get_node (inline) 7ms 0.027% 66.66% 583ms 2.24% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 583ms 2.24% 68.90% 583ms 2.24% [libchaste_cell_based.so] 47ms 0.18% 69.08% 583ms 2.24% std::_Rb_tree::_M_copy (inline) 191ms 0.73% 69.82% 572ms 2.20% __GI___libc_malloc 543ms 2.09% 71.90% 543ms 2.09% boost::numeric::ublas::c_vector::operator() 0 0% 71.90% 532ms 2.04% std::set::set (inline) 524ms 2.01% 73.92% 524ms 2.01% boost::numeric::ublas::same_impl_ex 217ms 0.83% 74.75% 522ms 2.01% std::_Rb_tree::_M_clone_node (inline) 3ms 0.012% 74.76% 515ms 1.98% Cell::GetMutationState 204ms 0.78% 75.54% 508ms 1.95% __cxxabiv1::__si_class_type_info::__do_dyncast 83ms 0.32% 75.86% 507ms 1.95% std::_Rb_tree::_M_erase 506ms 1.94% 77.81% 506ms 1.94% [libchaste_mesh.so] 353ms 1.36% 79.16% 491ms 1.89% std::vector::push_back (inline) 98ms 0.38% 79.54% 484ms 1.86% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.0077% 79.55% 483ms 1.86% NodeBasedCellPopulation::WriteVtkResultsToFile 5ms 0.019% 79.57% 420ms 1.61% AbstractCellProperty::IsSubType (inline) 0 0% 79.57% 412ms 1.58% std::_Rb_tree::_M_drop_node (inline) 0 0% 79.57% 409ms 1.57% std::set::~set (inline) 407ms 1.56% 81.13% 407ms 1.56% __strcmp_evex 15ms 0.058% 81.19% 405ms 1.56% boost::numeric::ublas::vector_binary::size (inline) 10ms 0.038% 81.23% 373ms 1.43% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.23% 366ms 1.41% std::_Rb_tree::_Alloc_node::operator() (inline) 363ms 1.39% 82.62% 363ms 1.39% std::_Rb_tree::_S_left (inline) 0 0% 82.62% 358ms 1.38% NodesOnlyMesh::ReMesh 3ms 0.012% 82.63% 347ms 1.33% NodesOnlyMesh::UpdateNodeIndices 6ms 0.023% 82.66% 318ms 1.22% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 82.66% 301ms 1.16% NodesOnlyMesh::UpdateBoxCollection 2ms 0.0077% 82.66% 295ms 1.13% Node::GetRadius 5ms 0.019% 82.68% 287ms 1.10% std::__new_allocator::deallocate (inline) 187ms 0.72% 83.40% 286ms 1.10% _int_malloc 2ms 0.0077% 83.41% 285ms 1.09% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 1ms 0.0038% 83.41% 282ms 1.08% Cell::HasCellProperty (inline) 0 0% 83.41% 281ms 1.08% CellPropertyCollection::HasProperty 3ms 0.012% 83.42% 270ms 1.04% DistributedBoxCollection::GetProcessOwningNode 0 0% 83.42% 268ms 1.03% boost::numeric::ublas::c_vector::assign (inline) 9ms 0.035% 83.46% 267ms 1.03% Cell::ReadyToDivide 239ms 0.92% 84.38% 266ms 1.02% boost::shared_ptr::shared_ptr (inline) 0 0% 84.38% 254ms 0.98% std::allocator_traits::deallocate (inline) 0 0% 84.38% 249ms 0.96% std::_Rb_tree::_M_put_node (inline) 62ms 0.24% 84.61% 248ms 0.95% __GI___libc_free 0 0% 84.61% 246ms 0.95% std::_Rb_tree::_Auto_node::_Auto_node (inline) 2ms 0.0077% 84.62% 243ms 0.93% NodesOnlyMesh::AddNodesToBoxes 77ms 0.3% 84.92% 237ms 0.91% std::__move_median_to_first (inline) 227ms 0.87% 85.79% 227ms 0.87% Node::CheckForNodeAttributes 0 0% 85.79% 226ms 0.87% boost::numeric::ublas::inner_prod (inline) 8ms 0.031% 85.82% 226ms 0.87% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 85.82% 226ms 0.87% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 85.82% 217ms 0.83% std::iter_swap (inline) 217ms 0.83% 86.65% 217ms 0.83% std::swap (inline) 214ms 0.82% 87.48% 214ms 0.82% boost::shared_ptr::operator-> (inline) 0 0% 87.48% 212ms 0.81% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 87.48% 210ms 0.81% VtkMeshWriter::WriteFiles 28ms 0.11% 87.58% 210ms 0.81% std::__insertion_sort (inline) 0 0% 87.58% 197ms 0.76% NodesOnlyMesh::ResizeBoxCollection 14ms 0.054% 87.64% 195ms 0.75% NodesOnlyMesh::IsANodeCloseToDomainBoundary 33ms 0.13% 87.76% 183ms 0.7% boost::numeric::ublas::vector_inner_prod::apply (inline) 90ms 0.35% 88.11% 180ms 0.69% std::__adjacent_find (inline) 0 0% 88.11% 180ms 0.69% std::__unique (inline) 0 0% 88.11% 180ms 0.69% std::unique (inline) 145ms 0.56% 88.67% 178ms 0.68% _int_free 0 0% 88.67% 177ms 0.68% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 88.67% 177ms 0.68% vtkStreamingDemandDrivenPipeline::Update 0 0% 88.67% 177ms 0.68% vtkXMLWriterBase::Write 0 0% 88.67% 176ms 0.68% std::__new_allocator::destroy (inline) 0 0% 88.67% 176ms 0.68% std::allocator_traits::destroy (inline) 0 0% 88.67% 175ms 0.67% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.67% 174ms 0.67% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.67% 173ms 0.66% std::_Rb_tree::_M_destroy_node (inline) 0 0% 88.67% 173ms 0.66% vtkExecutive::CallAlgorithm 0 0% 88.67% 172ms 0.66% vtkCompositeDataPipeline::ExecuteData 0 0% 88.67% 172ms 0.66% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.67% 172ms 0.66% vtkXMLUnstructuredDataWriter::ProcessRequest 8ms 0.031% 88.70% 168ms 0.65% AbstractCellProperty::IsType (inline) 3ms 0.012% 88.71% 160ms 0.61% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 5ms 0.019% 88.73% 153ms 0.59% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 88.73% 151ms 0.58% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.73% 151ms 0.58% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 88.73% 147ms 0.56% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 2ms 0.0077% 88.74% 143ms 0.55% AbstractCellPopulation::SetCellUsingLocationIndex 1ms 0.0038% 88.74% 142ms 0.55% std::_Rb_tree::clear (inline) 0 0% 88.74% 139ms 0.53% std::_Rb_tree::_M_insert_unique 0 0% 88.74% 139ms 0.53% std::set::insert (inline) 0 0% 88.74% 136ms 0.52% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.74% 136ms 0.52% Cell::GetCellId 7ms 0.027% 88.77% 132ms 0.51% NodeBasedCellPopulation::SetNode 13ms 0.05% 88.82% 131ms 0.5% boost::numeric::ublas::vector_reference::operator() (inline)